Two opposing models have been proposed for AID to deaminate either DNA or RNA. Although most data supports DNA deamination, there is no physical evidence for uracils in immunoglobulin genes. Here we demonstrate their presence by determining the sensitivity of DNA to digestion with uracil DNA glycosylase and abasic endonuclease. Using several methods of detection, we identified uracils in the variable and switch regions. Uracils were generated within 24 hours after B cell stimulation, were found on both DNA strands, and were enriched in hotspot motifs. This data provides direct evidence for the model that AID functions by deaminating cytosine in DNA. In addition, we have shown the XRCC1 protein is involved in repairing the uracils.